Cartoon about noncovalent interactions

Hydrogen bond

The hydrogen bond is also referred to as hydrogen bridge, and, as its name implies, it involves a hydrogen atom. Indeed, this is a particular case of a dipole-dipole interaction (an interaction established between polar molecules) that includes a hydrogen atom, and requires specific conditions to be established.

There are two requirements that have to occur in order to be established a hydrogen bond. Therefore, not all polar molecules having hydrogen atoms have the ability to establish this type of interaction... The first requirement that must be acomplished is the existence of a very electronegative atom in one of the involved molecules. When I say "very electronegative" I 'm referring to one of the 3 most electronegative atoms - oxygen, nitrogen or fluorine. This atom will function as an "acceptor" of hydrogen, due to the fact that it is very electronegative, and thus it will have a very high electron density on it, presenting a partial negative charge. The second condition that needs to occur is the existence of a hydrogen atom covalently bonded to a very electronegative atom. In this case, the latter acts as a "donor" of hydrogen, and the hydrogen will present partial positive charge because it is attached to a very electronegative atom.

So, what happens is an electrostatic attraction between opposite partial charges, settling the hydrogen bridge. In biochemistry, the hydrogen bonds, like the remaining non-covalent forces, are very important. The best known example concerns the interaction between complementary nitrogenous bases in DNA.

And now... despite having already written this in another post , I can not resist telling it again: ;)

Do you know how an electron commits suicide?

It jumps from the hydrogen bridge!

Dipole-dipole interaction

The dipole-dipole interaction, unlike the ionic bond (recently explained here in the blog ... ) involves non ionizable functional groups, ie without total positive or negative charges. It involves regions with partial charges...

It is a type of electrostatic interaction established between polar molecules, or at least between polar regions of biomolecules. As explained on a previous post about the concept of electronegativity, the presence of atoms with different electronegativities in a specific region of a molecule, will lead to inequalities in the distribution of the electronic cloud, which will, in turn, create regions with less electron density (and hence with partial positive charges) and regions with higher electron density (and hence with partial negative charges).

Thus, a region with a partial positive charge tends to interact electrostatically with a region of a partial negative charge, through a dipole-dipole bond.

Ionic bond

The ionic bond, also called salt bridge, it is, perhaps, the easiest non-covalent bond type to understand. As the name implies, it is an interaction that occurs between ions, i.e., between positive and negative charges. In biochemistry, the concept of ion is slightly different, because in a biomolecule (a protein, for example) we can have multiple regions with negative and/or positive charges. For this to happen just it is only necessary the presence of ionizable functional groups...

Therefore, when one biomolecule has a region with a negative charge (a phosphoryl or carboxyl group, for example), it can establish electrostatic interactions with a region of a biomolecule that presents a positive charge (e.g., amine or imidazole functional groups). This electrostatic attraction that occurs between the opposite charges is the ionic bond.

It is a type of interaction that occurs between polar molecules or at least between ionizable polar regions of biomolecules. As examples, we have the case of an interaction between a lysine and a glutamate in the interior of a protein or the interaction between DNA and histones, among many others...

Video about London Dispersion Forces

Intermolecular forces and melting/boiling point

One thing that tends to make confusion to my students is the relationship between non-covalent intermolecular forces and the melting/boiling point of a substance. In fact, how one can explain in a molecular point of view, the existence of the liquid and solid states? The answer lies precisely by the existence of intermolecular forces. Both states are characterized by a higher order spatial distribution of the molecules compared to the gaseous state. This order is a consequence of the attractions between the different molecules that make up a substance. Thus, in the liquid state, each molecule establishes various interactions (non-covalent!) with neighboring molecules, and in the solid state the amount of interactions is further increased.

When it is reached the melting/boiling point, which is going on is a transition from a state in which there are more intermolecular forces to one where there are fewer. In other words, what is being done is to provide energy to break the non-covalent forces established between the molecules, by increasing their kinetic energy.

Therefore, the greater the intensity of the non-covalent forces existing between the molecules, the greater the amount of energy required to break these interactions, and thus the higher the melting/boiling point.

I often ask to my students what happens when it is reached the boiling point of a substance, and the answer that I invariably get is: "You are breaking the bonds." The problem comes when I ask what kind of bonds, because usually their tendency is to say the covalent bonds. I, playfully, then tell them that if so, the water in the gaseous state is no longer H₂O, and then they realize that indeed that what it is cleaved are not the covalent bonds but the non-covalent ones.

In short, there is a direct relationship between intermolecular forces and melting/boiling point, and the greater the sum of these forces, the higher the melting/boiling point of a substance.

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Cartoon about non-covalent bonds

Noncovalent interactions (part 2)

As mentioned in my first post about the non-covalent bonds , they are something essential in biochemistry!

At one side, since they are weak forces, they allow dynamic communications between molecules or within the same molecule. In other words, since they are weak they may allow, for example, that two molecules interact temporarily with one another, or that certain macromolecules acquire specific conformations temporarily . But in either case, if you need to change this situation, it is not complicated as these are weak forces... Examples of the first situation are an interaction between a substrate and the active site of an enzyme (please note that in some cases the substrate can interact with the enzyme covalently!), an interaction between a receptor and its ligand, an interaction between two proteins , etc. . Examples of the latter are an enzymatic conformational changes induced by binding of a substrate or by binding of an allosteric modulator, a protein conformational changes in response to a pH change (which happens, for example, with phosphofructokinase -1 during lactic fermentation, and this is one of the factors associated with muscle fatigue...), etc.

But do not be fooled by the individual weakness of each non-covalent interaction. In fact, as in biochemistry we often deal with large molecules (polysaccharides, proteins, nucleic acids , for example) , there are numerous locations within those molecules that can interact with each other. Thus, they form a network of non-covalent interactions that is responsible for maintaining the 3D structure of these molecules. The sum of all forces becomes huge, giving a greater stability to biomolecules. This is why, for example, a protein acquires one or a few possible conformations, despite virtually there is an enormous number of protein conformations that could be present...
Finally, there is a very important aspect that is related to non-covalent forces that molecules may be involved with: its solubility! In fact, often when someone dissolves something in water (salt or sugar, for example), does not think on why the dissolution occured. The idea is quite simple... for a substance to dissolve in a particular solvent, the molecules that compose it must be able to interact with the molecules of the solvent, in an energetically way more favorable than their initial arrangement . For example, the sum of the network of interactions between the atoms of Na⁺ and Cl^- in the salt is less than the sum of the interactions of such ions with water molecules. Thus, in the presence of water the salt dissolves. And the reasoning is valid for any solute and/or solvent. Therefore it is said that "Like dissolves like" , which in reality tells us that the dissolution occurs when there is chemical affinity between the molecules of solute and solvent .